[gmx-users] g_rmsf => average over # of time frames ???

[Tsjerk Wassenaar]

Hi,

Lin, please think your questions over thoroughly in stead of flushing
every thought right to the mailing list. It also helps to stick to a
certain subject (reply) to make sure everything ends up in the same
thread. Maybe it's not a bad idea to read over
http://www.catb.org/esr/faqs/smart-questions.html (again).

Anyway, this question's quite valid :), and Marks answer is a bit
off... The reference structure for computing the RMSF is only used for
fitting; you'd also have seen this behaviour if you'd taken an average
structure from an equilibrium simulation. The fluctuations are around
the mean structure. The larger "fluctuations" in the first part of the
simulation are caused by the relaxation from the starting structure.
<oversimplification>If you think of the starting structure and the
'equilibrium structure' as position A and B, then the first part shows
you the mean squared deviation of the path from A to B around (A+B)/2,
whereas the next parts give you the mean squared deviation around
B</oversimplification>. Note that this gives you a means to assess
whether you've reached equilibrium, albeit not a sufficient measure.

Hope it helps,

Tsjerk


On Tue, Oct 26, 2010 at 8:24 AM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> If the reference structure from which the fluctuations are measured is taken
> from the -s file (check the documentation or code), then a non-equilibrium
> trajectory could well have this property w.r.t. a crystal structure.
>
> Mark
>
> ----- Original Message -----
> From: Chih-Ying Lin <chihying2008 at gmail.com>
> Date: Tuesday, October 26, 2010 15:55
> Subject: [gmx-users] g_rmsf => average over # of time frames ???
> To: gmx-users at gromacs.org
>
>>
>>
>> Hi
>>
>> From source code => gmx_rmsf.c
>
>> "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ",
>
>>     "deviation) of atomic positions ",
>
>>
>
>>     if (devfn) {
>
>>       /* Calculate RMS Deviation */
>
>>       for(i=0;(i<isize);i++) {
>
>> aid = index[i];
>
>> for(d=0;(d<DIM);d++) {
>
>>   rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
>
>> }
>
>>       }
>
>>     }
>
>>     count += 1.0;
>
>>
>
>> rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
>
>>
>
>>
>
>> Therefore, g_rmsf is the average of structure deviation over the time
>> frames.
>
>>
>
>> However, I issued the commands  ( C-alpha is selected )
>
>> g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg
>
>> g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o
>> RMSF-abc-100th-200th.xvg
>
>> g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o
>> RMSF-abc-200th-300th.xvg
>
>> g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o
>> RMSF-abc-300th-400th.xvg
>
>> g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o
>> RMSF-abc-400th-500th.xvg
>
>> g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o
>> RMSF-abc-500th-600th.xvg
>
>> g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o
>> RMSF-abc-600th-700th.xvg
>
>> g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o
>> RMSF-abc-700th-800th.xvg
>
>> g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o
>> RMSF-abc-800th-900th.xvg
>
>> g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o
>> RMSF-abc-900th-1000th.xvg
>
>>
>
>>
>
>> Also, (  C-alpha is selected )
>
>> g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o
>> RMSF-abc-0th-1000th.xvg
>
>>
>
>>
>
>>
>
>> Then I ploted,
>
>> RMSF-abc-0th-100th.xvg
>
>> RMSF-abc-100th-200th.xvg
>
>> RMSF-abc-200th-300th.xvg
>
>> RMSF-abc-300th-400th.xvg
>
>> RMSF-abc-400th-500th.xvg
>
>> RMSF-abc-500th-600th.xvg
>
>> RMSF-abc-600th-700th.xvg
>
>> RMSF-abc-700th-800th.xvg
>
>> RMSF-abc-800th-900th.xvg
>
>> RMSF-abc-900th-1000th.xvg
>
>>
>
>>
>
>> Also, I ploted
>
>> RMSF-abc-0th-1000th.xvg
>
>>
>
>>
>
>>
>
>> The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than
>> those from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg
>> / RMSF-abc-200th-300th.xvg / ......   / RMSF-abc-900th-1000th.xvg.......
>
>>
>
>>
>
>> It does not make sense... I supposed.....
>
>> Did I misunderstand something ?
>
>>
>
>>
>
>>
>
>> THank you
>
>> Lin
>
>>
>
>>
>
>>
>
>>
>
>>
>
>>
>
>>
>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands